[Biopython] Using Tabix on a bgzf file

[Peter Cock]

On Sunday, February 16, 2014, Vishnu Chilakamarri <vishnuc11j93 at gmail.com>
wrote:

> Hi Peter,
>
> I read your code on bgzf compression and the blog post. I used
> uniprot_sprot_varsplic.fasta.gz<
> ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz
> >as
> the example (from the EBI ftp) to compress in bgzf and then index
> using
> Tabix. Now the file I've gotten has a .tbi extension. I'm trying to parse
> the file but gives a preset not provided error and when I'm trying to
> access columns I'm getting indexes overlap error. Can you tell me where
> I've gone wrong?
>
> Thank you,
> Vishnu
>
>
Biopython doesn't (currently) use the tabix index (*.tbi) file.

Biopython's Bio.SeqIO indexing code uses the BGFZ compressed
sequence file directly. Using the SeqIO.index(...) function will make
an in memory index, using SeqIO.index_db(...) will make an index
in disk using SQLite. This system is quite separate from tabix
(and Biopython uses it for many many sequence files formats,
not just FASTA).

Peter